On 1 Aug 2012, at 02:02, Connolly, Colm wrote:
> Hi everybody,
>
> I've been trying to extract the individual ROIs from the Harvard-Oxford atlas included with FSL. I've successfully managed to do this by iterating through HarvardOxford-Cortical.xml which contains 48 labels that match the number of ROIs in HarvardOxford-cort-maxprob-thr25-1mm.nii.gz.
>
> I'm having problems doing the same thing with the subcortical atlas. HarvardOxford-sub-maxprob-thr25-1mm.nii.gz contains 58 ROIs but the HarvardOxford-Subcortical.xml contains only 20. Is this by design or mistake?
The image actually contains 21 ROIs as per the XML file, the label values being consistent with the MGH subcortical atlases label values. As Tren already pointed out the row number in the label file indicates the index in the XML file.
Hope that helps,
Dave
--
Dave Flitney
Oxford Centre for Functional MRI of the Brain
E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
URL: http://www.fmrib.ox.ac.uk/~flitney
|